1. OG-9, a novel mouse homeobox gene, was cloned and partially sequenced. Multiple species of OG-9 mRNA were found in 7-17 day old mouse embryos. One species of OG-9 mRNA was found in RNA only from adult striated muscle. 2. OG-2, a novel homeobox gene, was cloned and partially sequenced. OG-2 mRNA is expressed in 15-17 day mouse embryos. Two major species of OG-2 mRNA were detected in adult mouse striated muscle and trace levels of OG-2 mRNA were found in cardiac muscle. OG-2 mRNA was not detected in other tissues tested. 3. OG-12 is a novel homeobox gene that is expressed in 7-17 day mouse embryos and in most adult tissues tested. Two species of OG-12 cDNA were found, which correspond to alternatively spliced species of OG-12 mRNA. 4. OG-35 is a novel mouse homeobox gene that encodes a protein with a homeodomain that is 88 percent identical to the homeodomain of C. elegans unc-4, a protein that determines part of the synaptic circuit of a class of motor neurons. 5.OG-22 is a novel mouse homeobox gene that is similar to rat Cart-1. Two species of OG-22 cDNA were cloned that correspond to alternatively spliced species of OG-22 mRNA. OG-22 is expressed in the first brachial arch, snout, and tongue of 10-12 day mouse embryos and in adult in seminiferous epithelium of the testes. 6. A novel mouse homeobox gene, NK-1.2, was cloned that encodes a protein with a homeodomain that is closely related to the Drosophila NK- 1 and Sax 1 homeodomains. In 12-14 day mouse embryos, Nkx-1.2 RNA was found in the mesencephalon, myelencephalon, spinal cord, vertebrae, and ribs. In adults Nkx-1.2 mRNA is present in the seminiferous tubules and spermatozoa. 7. The patterns of expression of Brain-1, Brain-2, Brain-4, and Scip POU domain genes were determined in embryonic, postnatal, and adult brain. Expression of Brain-2, Brain-4, and Scip genes is restricted to the nervous system. Brain-1 is expressed in all regions of the adult brain, but is not restricted to the nervous system. Brain-2 is strongly expressed by all neuroepithelial cells in the brain.